Gene detail

Detailed information of OS493_020270-T1 in Lophelia pertusa

Genomic Location: scaffold_74:821463...824789
NR annotation: KAJ7384689.1, SNW domain-containing protein 1 [Desmophyllum pertusum]
Species Lophelia pertusa · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q13573	SNW domain-containing protein 1 OS=Homo sapiens OX=9606 GN=SNW1 PE=1 SV=1
Q9CSN1	SNW domain-containing protein 1 OS=Mus musculus OX=10090 GN=Snw1 PE=1 SV=3
Q5R7R9	SNW domain-containing protein 1 OS=Pongo abelii OX=9601 GN=SNW1 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0007118 (this species only)

Pfam domain

No Pfam domain signature was detected for OS493_020270-T1. This gene does have a gene model — the search simply returned no hit.

InterPro

InterPro term	Type	Description	Source
IPR017862 all species →	Family	SKI-interacting protein, SKIP	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12096 all species →	NUCLEAR PROTEIN SKIP-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000398 all species →	Biological Process	mRNA splicing, via spliceosome	Interproscan
GO:0005681 all species →	Cellular Component	spliceosomal complex	Interproscan

Search by domain instead of by gene. Any accession above (InterPro, Pfam, PANTHER, GO, KEGG) can be used as a query on the Functional Domain Search page, which searches all 148 annotated genomes at once.

KEGG pathway

No KEGG orthology assignment for OS493_020270-T1.

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of OS493_020270-T1 across 110 RNA-seq samples of Lophelia pertusa. Values are TPM (transcripts per million) from the StringTie quantification; one bar is one sample, grouped and coloured by condition, sorted by expression within each group.

110Samples

110TPM > 0

7Conditions

91.5Max TPM

45.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	38.22	68.73
polyp at pH7 6	18	18	41.47	91.54
coral polyp · control treatment	16	16	52.05	75.56
coral polyp · oil and dispersant treatment	16	16	52.49	75.34
coral polyp · oil treatment	16	16	50.54	68.20
coral polyp · dispersant treatment	16	16	34.96	78.52
Polyp	10	10	54.25	70.32

Per sample · hover a bar for the full sample record · show / hide the sample table

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	68.73
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	51.15
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	49.26
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	44.27
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	42.24
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	42.11
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	40.48
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	39.90
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	38.36
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	35.22
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	34.33
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.54
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.06
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.51
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.12
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.83
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.52
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.35
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	91.54
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	79.16
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	48.88
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	48.18
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	42.64
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	41.10
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	40.19
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	39.90
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	38.89
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.98
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.66
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.61
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.28
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.17
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.99
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.62
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.58
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.14
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	75.56
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	66.68
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	59.25
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	56.74
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	55.75
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	55.32
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	55.11
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	54.25
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	53.66
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	49.13
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	45.31
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	43.13
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	42.85
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	41.62
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	39.24
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	39.18
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	75.34
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	68.85
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	68.04
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	59.80
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	58.33
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	56.01
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	55.09
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	54.94
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	52.90
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	49.43
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	47.73
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	46.83
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	43.61
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	36.62
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	35.07
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	31.20
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	68.20
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	58.99
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	56.58
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	54.71
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	53.97
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	53.22
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	53.04
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	52.35
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	51.21
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	50.60
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	48.18
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	46.23
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	42.30
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	41.95
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	39.67
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	37.36
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	78.52
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	53.24
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	43.61
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	42.26
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	40.06
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	34.21
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	33.22
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	32.75
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	31.21
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	30.60
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.98
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.17
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.90
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.63
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.62
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.41
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	70.32
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	65.59
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	65.50
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	57.42
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	56.81
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	56.66
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	50.28
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	41.02
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	40.26
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	38.67

Source: CnidoSite RNA-seq expression matrices (LPERT_TPM, StringTie quantification over 110 runs), joined to SRA sample metadata. Samples whose tissue/treatment is not recorded in the source metadata are grouped by the descriptor carried in the expression matrix itself.